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Clinical Analysis

Colorimetric Detection of S1 Nuclease Activity using a Hairpin DNA with Split G-Quadruplex

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Pages 71-81 | Received 27 Jan 2023, Accepted 17 Mar 2023, Published online: 31 Mar 2023

References

  • Alsharabasy, A. M., A. Pandit, and P. Farras. 2021. Recent advances in the design and sensing applications of hemin/coordination polymer-based nanocomposites. Advcanced Materials 33:2003883. doi:10.1002/adma.202003883.
  • Cao, R., B. Li, Y. Zhang, and Z. Zhang. 2011. Naked-eye sensitive detection of nuclease activity using positively-charged gold nanoparticles as colorimetric probes. Chemical Communications (Cambridge, England) 47 (45):12301–3. doi:10.1039/c1cc15994a.
  • Ceska, T. A., and J. R. Sayers. 1998. Structure-specific DNA cleavage by 5' nucleases. Trends in Biochemical Sciences 23 (9):331–6. doi:10.1016/s0968-0004(98)01259-6.
  • Chen, X., L. Wang, F. He, G. Chen, L. Bai, K. He, F. Zhang, and X. Xu. 2021. Label-free colorimetric method for detection of vibrio parahaemolyticus by trimming the G-quadruplex DNAzyme with CRISPR/Cas12a. Analytical Chemistry 93 (42):14300–6. doi:10.1021/acs.analchem.1c03468.
  • Connelly, R. P., C. Verduzco, S. Farnell, T. Yishay, and Y. V. Gerasimova. 2019. Toward a rational approach to design split G-quadruplex probes. ACS Chemical Biology 14 (12):2701–12. doi:10.1021/acschembio.9b00634.
  • Deng, M., D. Zhang, Y. Zhou, and X. Zhou. 2008. Highly effective colorimetric and visual detection of nucleic acids using an asymmetrically split peroxidase DNAzyme. Journal of the American Chemical Society 130 (39):13095–102. doi:10.1021/ja803507d.
  • Fliess, A., H. Wolfes, A. Rosenthal, K. Schwellnus, H. Blöcker, R. Frank, and A. Pingoud. 1986. Role of thymidine residues in DNA recognition by the EcoRI and EcoRV restriction endonucleases. Nucleic Acids Research 14 (8):3463–74. doi:10.1093/nar/14.8.3463.
  • Fu, Y., C. Du, Q. Zhang, K. Xiao, X. Zhang, and J. Chen. 2022. Colorimetric and photocurrent-polarity-switching photoelectrochemical dual-mode sensing platform for highly selective detection of mercury ions based on the split G-Quadruplex-Hemin complex. Analytical Chemistry 94 (43):15040–7. doi:10.1021/acs.analchem.2c03084.
  • Grindley, N. D. F., K. L. Whiteson, and P. A. Rice. 2006. Mechanisms of site-specific recombination. Annual Review of Biochemistry 75:567–605. doi:10.1146/annurev.biochem.73.011303.073908.
  • Guo, Y., J. Chen, M. Cheng, D. Monchaud, J. Zhou, and H. Ju. 2017. A thermophilic tetramolecular G-quadruplex/hemin DNAzyme. Angewandte Chemie (International ed. in English) 56 (52):16636–40. doi:10.1002/anie.201708964.
  • Halford, S. E., and A. J. Goodall. 1988. Modes of DNA cleavage by the EcoRV restriction endonuclease. Biochemistry 27 (5):1771–7. doi:10.1021/bi00405a058.
  • He, C., J. L. Zhang, W. Li, and Y. Fu. 2018. Engineering oligonucleotide-based peroxidase mimetics for the colorimetric assay of S1 nuclease. Analytical Methods 10:1405–12. doi:10.1039/c7ay02830j.
  • Ishikawa, R., M. Yasuda, S. Sasaki, Y. Ma, K. Nagasawa, and M. Tera. 2021. Stabilization of telomeric G-quadruplex by ligand binding increases susceptibility to S1 nuclease. Chemical Communications (Cambridge, England) 57 (59):7236–9. doi:10.1039/d1cc03294a.
  • Kim, B. G., H. M. Evans, D. N. Dubins, and T. V. Chalikian. 2015. Effects of salt on the stability of a G-quadruplex from the human c-MYC promoter. Biochemistry 54 (22):3420–30. doi:10.1021/acs.biochem.5b00097.
  • Li, D., H. Xia, Y. Sun, W. Liu, W. Liu, J. Yu, G. Jing, J. Zhang, and W. Li. 2023. Colorimetric aptasensor for the sensitive detection of ochratoxin a based on a triple cascade amplification strategy. Analytica Chimica Acta 1237:340616. doi:10.1016/j.aca.2022.340616.
  • Li, T., E. Wang, and S. Dong. 2009. Potassium-lead-switched G-quadruplexes: A new class of DNA logic gates. Journal of the American Chemical Society 131 (42):15082–3. doi:10.1021/ja9051075.
  • Li, W., Y. Li, Z. Liu, B. Lin, H. Yi, F. Xu, Z. Nie, and S. Yao. 2016. Insight into G-quadruplex-hemin DNAzyme/RNAzyme: Adjacent adenine as the intramolecular species for remarkable enhancement of enzymatic activity. Nucleic Acids Research 44 (15):7373–84. doi:10.1093/nar/gkw634.
  • Liu, Y,., L. Wang, R. Ding, N. C. Sha, J. W. Seeman, and Canary, R. 2012. Templated synthesis of nylon nucleic acids and characterization by nuclease digestion. Chemical Science 3 (6):1930–7. doi:10.1039/c2sc20129a.
  • McLaughlin, L., W. F. Benseler, E. Graeser, N. Piel, and S. Scholtissek. 1987. Effects of functional group changes in the EcoRI recognition site on the cleavage reaction catalyzed by the endonuclease. Biochemistry 26 (23):7238–45. doi:10.1021/bi00397a007.
  • Nishino, T., and K. Morikawa. 2002. Structure and function of nucleases in DNA repair: Shape, grip and blade of the DNA scissors. Oncogene 21 (58):9022–32. doi:10.1038/sj.onc.1206135.
  • Nishio, M., K. Tsukakoshi and, K. Ikebukuro. 2021. G-quadruplex: Flexible conformational changes by cations, pH, crowding and its applications to biosensing. Biosensors & Bioelectronics 178:113030. doi:10.1016/j.bios.2021.113030.
  • Qu, X. M., D. Zhu, G. B. Yao, S. Su, J. Chao, H. J. Liu, X. L. H. Zuo, L. H. Wang, J. Shi, L. Wang, et al. 2017. An exonuclease III-powered, on-particle stochastic DNA walker. Angewandte Chemie-International Edition 56:1855–8. doi:10.1002/ange.201611777.
  • Shahsavar, K., E. Shokri, and M. Hosseini. 2022. Sensitive colorimetric detection of miRNA‑155 via G‑quadruplex DNAzyme decorated spherical nucleic acid. Mikrochimica Acta 189 (9):357. doi:10.1007/s00604-022-05455-7.
  • Shi, L., X. M. Ma, H. J. Xie, Y. J. Qin, Y. Huang, Y. Y. Zhang, L. Z. Sun, J. Yang, and G. X. Li. 2023. Engineering m6A demethylation-activated DNAzyme for visually and sensitively sensing fat mass and obesity-associated protein. Biosensors & Bioelectronics 222:115007. doi:10.1016/j.bios.2022.115007.
  • Simonsson, T. 2001. G-quadruplex DNA structures-variations on a theme. Biological Chemistry 382 (4):621–8. doi:10.1515/BC.2001.073.
  • Wei, Z. H., Y. F. Yu, S. Q. Hu, X. Y. Yi, and J. X. Wang. 2021. Bifunctional diblock DNA-mediated synthesis of nanoflower shaped photothermal nanozymes for a highly sensitive colorimetric assay of cancer cells. ACS Applied Materials & Interfaces 13 (14):16801–11. doi:10.1021/acsami.0c21109.
  • West, S. C. 2003. Molecular views of recombination proteins and their control. Nature Reviews. Molecular Cell Biology 4 (6):435–45. doi:10.1038/nrm1127.
  • Xi, H., M. Juhas, and Y. Zhang. 2020. G-quadruplex based biosensor: A potential tool for SARS-CoV-2 detection. Biosensors & Bioelectronics 167:112494. doi:10.1016/j.bios.2020.112494.
  • Xia, S. Y., F. X. Wu, L. Cheng, H. B. Bao, W. P. Gao, J. Duan, W. X. Niu, and G. B. Xu. 2023. Maneuvering the peroxidase-like activity of palladium-based nanozymes by alloying with oxophilic bismuth for biosensing. Small 19 (6):e2205997. doi:10.1002/smll.202205997.
  • Xu, X., M. S. Han, and C. A. Mirkin. 2007. A gold-nanoparticle-based real-time colorimetric screening method for endonuclease activity and inhibition. Angewandte Chemie (International ed. in English) 46 (19):3468–70. doi:10.1002/anie.200605249.
  • Yoo, S. M., T. Kang, B. Kim, and S. Y. Lee. 2011. Detection of single nucleotide polymorphisms by a gold nanowire-on-film SERS sensor coupled with S1 nuclease treatment. Chemistry (Weinheim an der Bergstrasse, Germany) 17 (31):8657–62. doi:10.1002/chem.201003372.
  • Zhong, Z. T., Y. F. He, Y. J. Tang, G. Ashraf, H. Yang, W. Chen, B. Liu, G. P. Wang, and Y. D. Zhao. 2022. Terminal deoxynucleotidyl transferase associated with split G-quadruplex/hemin deoxyribozyme amplification detection for various contaminants in milk based on pregnancy test strip platform. Biosensors & Bioelectronics 216:114644. doi:10.1016/j.bios.2022.114644.

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